| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/bgruening/glimmer_knowledge_based/glimmer_knowledge_based/3.02 (this tool) |
| glimmer_knowledge_based |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| glimmer | 3.02 | package |
| biopython | 1.70 | package |
| Additional information about this tool |
glimmer3
--max_olap $max_olap
--gene_len $gene_len
--threshold $threshold
#if float( str($gc_percent) ) > 0.0:
--gc_percent $gc_percent
#end if
#if $stop_codon_opts.stop_codon_opts_selector == "gb":
--trans_table '${stop_codon_opts.genbank_gencode}'
#else:
--stop_codons '${stop_codon_opts.stop_codons}'
#end if
--start_codons '$start_codons'
$linear
$no_indep
$extend
'$seq_input'
'$icm_input'
glimmer_output
&&
#if $report:
cp glimmer_output.predict '$report_output' &&
#end if
#if $detailed_report:
cp glimmer_output.detail '$detailed_output' &&
#end if
## convert prediction to FASTA sequences
python '$__tool_directory__/glimmer2seq.py' glimmer_output.predict '$seq_input' '$genes_output'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
seq_input: streptomyces_Tue6071_plasmid_genomic.fasta icm_input: streptomyces_Tu6071_plasmid_genes.icm max_olap: 50 gene_len: 90 threshold: 30 gc_percent: 0.0 linear: True no_indep: False extend: False start_codons: atg,gtg,ttg stop_codon_opts|genbank_gencode: 11 report: True detailed_report: True |
name: value name: value name: value |
streptomyces_Tue6071_plasmid_genomic.fasta streptomyces_Tu6071_plasmid_genes.icm value |